Understanding the Plot

• Track 1 (Gene Quality): Shows genes colored by assembly quality
  • Green (Excellent): ≥95% identity
  • Yellow (Good): 85-95% identity
  • Orange (Fair): 70-85% identity
  • Red (Poor): <70% identity
• Track 2 (Contig Mapping): Shows which assembly contigs map to the reference
• Track 3 (Coverage Depth): Shows how many times each position is covered
• Track 4 (Alignment Identity): Shows sequence identity percentage across the genome
• Track 5 (Misassemblies): Highlights regions with assembly errors
  • Bottom layer: Contig positions (colored bars showing which contig)
  • Upper layers: Overlaps, Gaps, and Inversions

Interactive Features

• Click on genes in Track 1 to view detailed alignments
• Hover over any element to see detailed information
• Zoom: Click and drag to select a region, double-click to reset
• Pan: Use the pan tool in the toolbar